Plant Circular RNA Database

Detail information of Os12g0607000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os12g0607000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_012245
					
						Alias
						Os12circ10540
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 25642144-25644267  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Os12g0607000						
					
						Parent gene annotation
						
							Similar to homocysteine S-methyltransferase-2. (Os12t0607000-01)
;Similar to Homocysteine S-methyltransferase 2 (EC 2.1.1.10) (S-
 methylmethionine:homocysteine methyltransferase 2) (SMM:Hcy S- 
methyltransferase 2) (ZmHMT-2). (Os12t0607000-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0607000_circ_g.1 Os12g0607000_circ_g.2 Os12g0607000_circ_g.4 Os12g0607000_circ_g.5 Os12g0607000_circ_g.6 Os12g0607000_circ_g.7 						
					
						Support reads
						2
					
						Tissues
						panicle
					
						Exon boundary  
						
							No-No							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Os12t0607000-02:5
Os12t0607000-01:5

General Information
CircRNA Name	Os12g0607000_circ_g.3
ID in PlantcircBase	osa_circ_012245
Alias	Os12circ10540
Organism	Oryza sativa
Position	chr12: 25642144-25644267 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl
Parent gene	Os12g0607000
Parent gene annotation	Similar to homocysteine S-methyltransferase-2. (Os12t0607000-01) ;Similar to Homocysteine S-methyltransferase 2 (EC 2.1.1.10) (S- methylmethionine:homocysteine methyltransferase 2) (SMM:Hcy S- methyltransferase 2) (ZmHMT-2). (Os12t0607000-02)
Parent gene strand	+
Alternative splicing	Os12g0607000_circ_g.1 Os12g0607000_circ_g.2 Os12g0607000_circ_g.4 Os12g0607000_circ_g.5 Os12g0607000_circ_g.6 Os12g0607000_circ_g.7
Support reads	2
Tissues	panicle
Exon boundary	No-No "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Os12t0607000-02:5 Os12t0607000-01:5

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							GAGTGGAGACTCGTTAATTGAATGTGCTACTATTGCTAATGGGTGTTCGAAGGTTGGTGCAGTT
GGAATAAATTGCACACCTCCAAGATTTATCCATGGCctgaacgacccgctctggagcgccaagt
gcctcctctcctccccgcacctcgtccgcaaggtcagcccgcaatctggcgatcatctcgcctg
tgttcttc

									
								

					

						Assembled circRNA sequence  
						
							NA
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							NA						
					

						Genomic sequence
						
							CTGAACGACCCGCTCTGGAGCGCCAAGTGCCTCCTCTCCTCCCCGCACCTCGTCCGCAAGGTCA
GCCCGCAATCTGGCGATCATCTCGCCTGTGTTCTTCCTGCTCGTTACGATTCCTCCTCTAGTCT
AGCATTCGGTCCTTTTTGTTTTGTCTCGTGCTATCTGACGAATCTGTGGAACTGGAGTAGAACA
GCAGCGATGCGTTCGCCTTGATTCTTGATGCGAGCGAGCATTGTTAACCAAAAAAAAAAAAGAA
GAGAAGTTATTTAAGATTTGGAAATAAACGACTAGATCAATTGAAGCAGTAAGGGTTATGAAAT
TGATAGGTCACTAGTTTACTGGAGTAGGGAAAAGTTTTTTTCTGCTTGCCCCTAGAGTGTTGGA
ACTGGGAAATATCTTGTTCTAAAAAGAATATTAAAAAGAGCATTGGAAATGTCCCCACGGTTCC
ATTATAATAAGCTAATTGCTATACCATGGACAGGACAGTATCAAACAAGTGTTTCTTTTTACCA
ACTCTTTTTTTAAAACTAAAACTTTTTTTTTACTGAGTGGAGTACTCCATTCGTCTAAAAAAAC
CAACCTAAATTGGAGGTGATATTTCCTAGTATAACGAACATTGGTTTTTTTTGGGACGGGTGGA
GTAGTAAAGAAGGGGAAAAAACCCAGCAATTTTCTGTGCTTCTACTTCTGTGGACTGTCTGATT
TTGGGAGTTCAATGATGTTTTGAAGGATTGACTTGATACGCGAGTCAAGCATGCCGGCTAGGTG
CTTTTGTGCTGTCTTTCTCCGAAGGTAGTCTTGTAGGATAAAGTGCAGACCAGCTGCTGAATCT
GCCCACAGCATTTGCCAACTGGAGTATATGCCAGTTGCCAAACTTATTCTGGCATTTTGGGATA
GAATTGAATTCTTATTCCAAAGCATAATTGAAGTCTTAACTGTTTTCCATGACCTGAGCTGAGA
TCTGGGGGGATTGGCCTTGCTGGTCCAAGTTTCATGGGCCATGTATCCTGGTCCTAGTCTGTCT
GTTTTCTGTCCTTTCAGATGATAATTGTGGATTGGCATGTCACAATTACCTGGTACTGTTATGT
GAAATAATATGAGAACTATTACTTAAAATGCACAGATTTTTATATTTTTGCAGTGCTAAGGAGT
TGCTAACTTTCCTTTTTTTTTTTCCTCTGCTGTATGTACCTAATAAATGTAGTGTACTATTTTC
GATCTGACCAATTATTTTGCATGCAAAGAGCTGTTTACAGATTATGACATCATACATTCTCCTT
ATGTGATGGAACAGGTCCATTTAGACTACCTAGAAGCAGGTGCAAATATCATAATCACAGCGTC
ATACCAGGTCAATTATATATTTCCACGCATTTTTCCAGTATATATGATATTCTTGTATGAACAG
TTCTAATATATTTGATGTTGCAGGCTACAATTCAAGGCTTTGAATCCAAGGGATTTTCAAAAGA
ACAAAGTGAAGACTTGCTCGCAAAGAGTGTTGAGATTGCACGTGAAGCGCGTGACATGTTTCTG
AAGGAACATTCAGATCGTCCCATACAACATCCTATCCTGGTTGCAGCTTCCATTGGAAGTTATG
GGGCCTATCTTGCTGACGGCTCTGAGTACAGGTACTTAACTACTTAATAGAGCAGAGCACTCAT
TTTCATGTATTGCTTCTGGGTAATCACTGTTTCTCTGGTGTTGTTAGTGGGGATTATGGCGAAG
CTGGCACGTTAGAATTCCTGAAAGATTTTCATAAGCGAAGGCTGGAGGTTCTTGCGGAAGCAGG
TCCTGATTTGATCGCCTTTGAAACAATTCCCAACAAATTGGAAGCTCAGGTATGTTATTCATTA
CTACTTACACCAGGGATCTTTTGCCTCTCATTTAACAATGTGTTCTTACAAAATAATCTCTATT
GTTTCGCTTGCTGGTCTTTAGGCTTACGTTGAACTTCTTGACGAATGTAACATCAGTATCCCTG
CATGGTTCTCATTTAATTCAAAAGATGGAGTTCACATTGTGAGTGGAGACTCGTTAATTGAATG
TGCTACTATTGCTAATGGGTGTTCGAAGGTTGGTGCAGTTGGAATAAATTGCACACCTCCAAGA
TTTATCCATGGC
						
					

			
		

Sequences
Splice junction sequence	GAGTGGAGACTCGTTAATTGAATGTGCTACTATTGCTAATGGGTGTTCGAAGGTTGGTGCAGTT GGAATAAATTGCACACCTCCAAGATTTATCCATGGCctgaacgacccgctctggagcgccaagt gcctcctctcctccccgcacctcgtccgcaaggtcagcccgcaatctggcgatcatctcgcctg tgttcttc
Assembled circRNA sequence	NA The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	NA
Genomic sequence	CTGAACGACCCGCTCTGGAGCGCCAAGTGCCTCCTCTCCTCCCCGCACCTCGTCCGCAAGGTCA GCCCGCAATCTGGCGATCATCTCGCCTGTGTTCTTCCTGCTCGTTACGATTCCTCCTCTAGTCT AGCATTCGGTCCTTTTTGTTTTGTCTCGTGCTATCTGACGAATCTGTGGAACTGGAGTAGAACA GCAGCGATGCGTTCGCCTTGATTCTTGATGCGAGCGAGCATTGTTAACCAAAAAAAAAAAAGAA GAGAAGTTATTTAAGATTTGGAAATAAACGACTAGATCAATTGAAGCAGTAAGGGTTATGAAAT TGATAGGTCACTAGTTTACTGGAGTAGGGAAAAGTTTTTTTCTGCTTGCCCCTAGAGTGTTGGA ACTGGGAAATATCTTGTTCTAAAAAGAATATTAAAAAGAGCATTGGAAATGTCCCCACGGTTCC ATTATAATAAGCTAATTGCTATACCATGGACAGGACAGTATCAAACAAGTGTTTCTTTTTACCA ACTCTTTTTTTAAAACTAAAACTTTTTTTTTACTGAGTGGAGTACTCCATTCGTCTAAAAAAAC CAACCTAAATTGGAGGTGATATTTCCTAGTATAACGAACATTGGTTTTTTTTGGGACGGGTGGA GTAGTAAAGAAGGGGAAAAAACCCAGCAATTTTCTGTGCTTCTACTTCTGTGGACTGTCTGATT TTGGGAGTTCAATGATGTTTTGAAGGATTGACTTGATACGCGAGTCAAGCATGCCGGCTAGGTG CTTTTGTGCTGTCTTTCTCCGAAGGTAGTCTTGTAGGATAAAGTGCAGACCAGCTGCTGAATCT GCCCACAGCATTTGCCAACTGGAGTATATGCCAGTTGCCAAACTTATTCTGGCATTTTGGGATA GAATTGAATTCTTATTCCAAAGCATAATTGAAGTCTTAACTGTTTTCCATGACCTGAGCTGAGA TCTGGGGGGATTGGCCTTGCTGGTCCAAGTTTCATGGGCCATGTATCCTGGTCCTAGTCTGTCT GTTTTCTGTCCTTTCAGATGATAATTGTGGATTGGCATGTCACAATTACCTGGTACTGTTATGT GAAATAATATGAGAACTATTACTTAAAATGCACAGATTTTTATATTTTTGCAGTGCTAAGGAGT TGCTAACTTTCCTTTTTTTTTTTCCTCTGCTGTATGTACCTAATAAATGTAGTGTACTATTTTC GATCTGACCAATTATTTTGCATGCAAAGAGCTGTTTACAGATTATGACATCATACATTCTCCTT ATGTGATGGAACAGGTCCATTTAGACTACCTAGAAGCAGGTGCAAATATCATAATCACAGCGTC ATACCAGGTCAATTATATATTTCCACGCATTTTTCCAGTATATATGATATTCTTGTATGAACAG TTCTAATATATTTGATGTTGCAGGCTACAATTCAAGGCTTTGAATCCAAGGGATTTTCAAAAGA ACAAAGTGAAGACTTGCTCGCAAAGAGTGTTGAGATTGCACGTGAAGCGCGTGACATGTTTCTG AAGGAACATTCAGATCGTCCCATACAACATCCTATCCTGGTTGCAGCTTCCATTGGAAGTTATG GGGCCTATCTTGCTGACGGCTCTGAGTACAGGTACTTAACTACTTAATAGAGCAGAGCACTCAT TTTCATGTATTGCTTCTGGGTAATCACTGTTTCTCTGGTGTTGTTAGTGGGGATTATGGCGAAG CTGGCACGTTAGAATTCCTGAAAGATTTTCATAAGCGAAGGCTGGAGGTTCTTGCGGAAGCAGG TCCTGATTTGATCGCCTTTGAAACAATTCCCAACAAATTGGAAGCTCAGGTATGTTATTCATTA CTACTTACACCAGGGATCTTTTGCCTCTCATTTAACAATGTGTTCTTACAAAATAATCTCTATT GTTTCGCTTGCTGGTCTTTAGGCTTACGTTGAACTTCTTGACGAATGTAACATCAGTATCCCTG CATGGTTCTCATTTAATTCAAAAGATGGAGTTCACATTGTGAGTGGAGACTCGTTAATTGAATG TGCTACTATTGCTAATGGGTGTTCGAAGGTTGGTGCAGTTGGAATAAATTGCACACCTCCAAGA TTTATCCATGGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.159571332

Conservation Information
Conserved circRNAs	NA
PMCS	0.159571332

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015

circRNA

Detail information of Os12g0607000_circ_g.3

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